AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0268200


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268200 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268200 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268200 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268200 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0268200 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0268200 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0268200 MtrunA17_Chr6g0451331 90.323 31 3 0 24 54 41 71 5.28e-14 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268200 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0268200 ATCG00560.1 97.297 37 1 0 68 104 2 38 3.75e-19 73.9

Find 27 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTTAGCTTACGATGTATT+TGG 0.244623 2_2:-70127482 Msa0268200:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 2_2:+70127220 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 2_2:+70127516 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 2_2:-70127565 Msa0268200:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 2_2:-70127617 Msa0268200:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 2_2:-70127524 Msa0268200:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 2_2:+70127517 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 2_2:-70127162 Msa0268200:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 2_2:+70127449 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 2_2:+70127214 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 2_2:+70127559 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 2_2:-70127608 Msa0268200:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 2_2:+70127231 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 2_2:-70127161 Msa0268200:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 2_2:-70127633 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 2_2:-70127503 Msa0268200:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 2_2:+70127454 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 2_2:+70127455 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 2_2:-70127504 Msa0268200:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 2_2:-70127520 Msa0268200:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 2_2:+70127453 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 2_2:+70127153 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 2_2:-70127626 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 2_2:-70127525 Msa0268200:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 2_2:+70127521 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 2_2:+70127520 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 2_2:-70127160 Msa0268200:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG - chr2_2:70127355-70127374 Msa0268200:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG + chr2_2:70127545-70127564 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG + chr2_2:70127546-70127565 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG + chr2_2:70127304-70127323 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG - chr2_2:70127358-70127377 Msa0268200:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG + chr2_2:70127459-70127478 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG - chr2_2:70127162-70127181 Msa0268200:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG + chr2_2:70127171-70127190 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG + chr2_2:70127281-70127300 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG - chr2_2:70127305-70127324 Msa0268200:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG + chr2_2:70127331-70127350 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG + chr2_2:70127410-70127429 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG - chr2_2:70127245-70127264 Msa0268200:intron 35.0%
TGTAAAATACTCGTTTGGAC+GGG + chr2_2:70127276-70127295 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG + chr2_2:70127277-70127296 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG - chr2_2:70127287-70127306 Msa0268200:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG + chr2_2:70127317-70127336 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG + chr2_2:70127405-70127424 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG - chr2_2:70127405-70127424 Msa0268200:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG + chr2_2:70127411-70127430 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG - chr2_2:70127409-70127428 Msa0268200:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG + chr2_2:70127499-70127518 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG + chr2_2:70127510-70127529 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG + chr2_2:70127516-70127535 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG - chr2_2:70127202-70127221 Msa0268200:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG + chr2_2:70127213-70127232 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG + chr2_2:70127214-70127233 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG + chr2_2:70127275-70127294 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG - chr2_2:70127322-70127341 Msa0268200:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG + chr2_2:70127386-70127405 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG + chr2_2:70127393-70127412 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG - chr2_2:70127449-70127468 Msa0268200:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG + chr2_2:70127455-70127474 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG + chr2_2:70127456-70127475 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG + chr2_2:70127577-70127596 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG - chr2_2:70127203-70127222 Msa0268200:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG - chr2_2:70127223-70127242 Msa0268200:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG - chr2_2:70127224-70127243 Msa0268200:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG - chr2_2:70127378-70127397 Msa0268200:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG - chr2_2:70127448-70127467 Msa0268200:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG - chr2_2:70127565-70127584 Msa0268200:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG - chr2_2:70127566-70127585 Msa0268200:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG - chr2_2:70127567-70127586 Msa0268200:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG + chr2_2:70127209-70127228 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG - chr2_2:70127419-70127438 Msa0268200:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG - chr2_2:70127110-70127129 Msa0268200:CDS 55.0%
CCAACCCGCAATGAATAGGG+AGG + chr2_2:70127210-70127229 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG - chr2_2:70127207-70127226 Msa0268200:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG - chr2_2:70127427-70127446 Msa0268200:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG - chr2_2:70127119-70127138 Msa0268200:CDS 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70127108 70127641 70127108 ID=Msa0268200;Name=Msa0268200
chr2_2 mRNA 70127108 70127641 70127108 ID=Msa0268200-mRNA-1;Parent=Msa0268200;Name=Msa0268200-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr2_2 exon 70127464 70127641 70127464 ID=Msa0268200-mRNA-1:exon:22518;Parent=Msa0268200-mRNA-1
chr2_2 exon 70127108 70127258 70127108 ID=Msa0268200-mRNA-1:exon:22517;Parent=Msa0268200-mRNA-1
chr2_2 five_prime_UTR 70127625 70127641 70127625 ID=Msa0268200-mRNA-1:five_prime_utr;Parent=Msa0268200-mRNA-1
chr2_2 CDS 70127464 70127624 70127464 ID=Msa0268200-mRNA-1:cds;Parent=Msa0268200-mRNA-1
chr2_2 CDS 70127108 70127258 70127108 ID=Msa0268200-mRNA-1:cds;Parent=Msa0268200-mRNA-1
Gene Sequence

>Msa0268200

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0268200

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN